Masaoka was a key player in JACL's decision to cooperate with the Japanese American internment during the war, seeing that resistance would be counterproductive and increase the tension between the Nisei and the FDR Administration. In his position as a national spokesman, he urged cooperation and opposed legal challenges to the government and advised the government on how to run the camps (thus to reduce friction between the internees and their captors). He also advocated the segregation of so‑called "troublemakers," though the War Relocation Authority cast the net more broadly than Masaoka had anticipated. The government used him as their liaison with the entire Japanese American population in the camps, although he himself was never imprisoned in a camp.

Masaoka was involved in leading the call for the formation of the Nisei100th Battalion and 442nd Regimental Combat Team, and later served as publicist for the highly decorated volunteer units, so that the contributions (and heavy price paid) of the Japanese Americans would be known nationwide.

He later served as technical consultant for the 1951 film Go For Broke! which not only portrayed the heroics of the 442nd RCT and 100th Battalion, but also starred several veterans of the 442nd.

Near the end of his life, Masaoka strongly implied (without directly stating) that the government had pressured him to make statements and "suggestions" to go along with their policies. In a PBS interview, he said "it was a kind of a shibai . . .We were pretty desperate." Shibai (芝居) is Japanese for performance or show.

In 1950, Masaoka was involved in successfully lobbying for the rights of the Issei (Japanese immigrants) to naturalize as citizens.[1] In 1952 he worked with the ACLU to bring a case in his mother's name, Masaoka vs. the State of California, to the California State Supreme Court that was one of the two cases that overturned the Alien Land Law (Masaoka v. People, 39 Cal.2d 883). He represented the JACL as a founding member of the Leadership Council on Civil Rights, and joined Dr. Martin Luther King's 1963 March on Washington. With his own consulting firm, Mike Masaoka Associates, he also lobbied on behalf of American and Japanese commercial interests.

In 1972 he left JACL to become a full‑time lobbyist. His autobiography, They Call Me Moses Masaoka, written with Bill Hosokawa, was published in 1987. Associates considered the title a sign of his ego, though the title was originally bestowed derisively by political opponents during the 1940s. Masaoka noted with ironic humor that, unlike Moses, he led his people on a journey from the promised land of California to desert internment camps.

Masaoka was married to Etsu Mineta Masaoka, the elder sister of Secretary of Transportation and Congressman Norman Mineta. Masaoka died in Washington, DC in 1991.[1]